User: stuart

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stuart10
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Posts by stuart

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Comment: C: DESeq2 outlier flagging with 2 replicates
... Thank you Michael. However, I found that `mcols(dds)$maxCooks` was all NAs by default when n=2, so I added it with: ``` mcols(dds)$maxCooks <- apply(assays(dds)[["cooks"]],1,max) ``` I hope this is equivalent to the normal calculation. Best, Stuart ...
written 5 months ago by stuart10
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DESeq2 outlier flagging with 2 replicates
... Hi all, We have a 2-factor, 2 levels per factor experimental design with 2 replicates per covariate combination (so 8 samples total, n=2 per cell) that we are analysing using DESeq2. Normally DESeq2 generates a Cook's distance for each replicate within a cell (by "cell" I mean unique combination ...
deseq2 written 5 months ago by stuart10 • updated 5 months ago by Michael Love26k
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Comment: C: Interaction effect sizes from DEXseq
... Ah, I see now, thanks for the clarification. Actually I just realised that mcols(dxrTEST1)$description gives some of this information, but it's useful to know where and when VST is applied too. ...
written 18 months ago by stuart10
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Comment: C: Interaction effect sizes from DEXseq
... Hi Alejandro, Thanks a lot, that's really helpful. Just a related question on the results object, as I want to make sure I genuinely understand how the log2fold-change is calculated: if I set gene_1:exon1 to be upregulated ~10-fold specifically in mut=='A' and treat='trt' by inserting some higher ...
written 18 months ago by stuart10
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Interaction effect sizes from DEXseq
... Dear all, I have a multifactorial experimental design (3 mutants and 2 treatments) am trying to obtain the difference of differences for exon usage. I can obtain p-values but not the fold-change of expression that is attributable to the interaction between mutant and treatment. I hope this makes se ...
dexseq multiple factor design written 18 months ago by stuart10 • updated 18 months ago by Alejandro Reyes1.7k
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Comment: C: Setting contrasts in limma where null hypothesis is that Test = 2 x Control
... Thank you very much, this was really helpful. The duplicated genes show an average ~ +0.8 logFC. This is less than +1.0 probably due to homeostatic mechanisms at play, which indicates that I should treat duplicated genes that are downregulated from the logFC +1.0 baseline with caution. Nonetheless ...
written 3.8 years ago by stuart10
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Setting contrasts in limma where null hypothesis is that Test = 2 x Control
... Hello, I am analysing RNA-seq data to find differentially expressed genes between a wild-type (Ctl) and mutant (Mut). The mutant has a large DNA duplication encompassing several hundred genes, so they always come up as ~2x upregulated but this is not biologically interesting. Hence the H0 (null) fo ...

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